niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_surf2volseg.py

@@ -0,0 +1,487 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SURF2VOLSEG_METADATA = Metadata(
+    id="5311f8712d7d6a5ffead8a7275ff29df715e3532.boutiques",
+    name="mri_surf2volseg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSurf2volsegParameters = typing.TypedDict('MriSurf2volsegParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_surf2volseg"],
+    "input_segmentation": typing.NotRequired[InputPathType | None],
+    "output_segmentation": typing.NotRequired[str | None],
+    "source_segmentation": typing.NotRequired[InputPathType | None],
+    "lh_white_surf": typing.NotRequired[InputPathType | None],
+    "lh_pial_surf": typing.NotRequired[InputPathType | None],
+    "rh_white_surf": typing.NotRequired[InputPathType | None],
+    "rh_pial_surf": typing.NotRequired[InputPathType | None],
+    "lh_cortex_mask": typing.NotRequired[InputPathType | None],
+    "rh_cortex_mask": typing.NotRequired[InputPathType | None],
+    "fix_presurf_ribbon": typing.NotRequired[InputPathType | None],
+    "label_cortex": bool,
+    "label_wm": bool,
+    "label_wm_unknown": typing.NotRequired[list[float] | None],
+    "lh_annotation": typing.NotRequired[InputPathType | None],
+    "rh_annotation": typing.NotRequired[InputPathType | None],
+    "wmparc_dmax": typing.NotRequired[float | None],
+    "rip_unknown": bool,
+    "hypo_as_wm": bool,
+    "hashres": typing.NotRequired[float | None],
+    "nhops": typing.NotRequired[float | None],
+    "help_flag": bool,
+    "version_flag": bool,
+    "crs_test": typing.NotRequired[list[float] | None],
+    "ctab_file": typing.NotRequired[InputPathType | None],
+    "threads_number": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_surf2volseg": mri_surf2volseg_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class MriSurf2volsegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_surf2volseg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_surf2volseg_params(
+    input_segmentation: InputPathType | None = None,
+    output_segmentation: str | None = None,
+    source_segmentation: InputPathType | None = None,
+    lh_white_surf: InputPathType | None = None,
+    lh_pial_surf: InputPathType | None = None,
+    rh_white_surf: InputPathType | None = None,
+    rh_pial_surf: InputPathType | None = None,
+    lh_cortex_mask: InputPathType | None = None,
+    rh_cortex_mask: InputPathType | None = None,
+    fix_presurf_ribbon: InputPathType | None = None,
+    label_cortex: bool = False,
+    label_wm: bool = False,
+    label_wm_unknown: list[float] | None = None,
+    lh_annotation: InputPathType | None = None,
+    rh_annotation: InputPathType | None = None,
+    wmparc_dmax: float | None = None,
+    rip_unknown: bool = False,
+    hypo_as_wm: bool = False,
+    hashres: float | None = None,
+    nhops: float | None = None,
+    help_flag: bool = False,
+    version_flag: bool = False,
+    crs_test: list[float] | None = None,
+    ctab_file: InputPathType | None = None,
+    threads_number: float | None = None,
+) -> MriSurf2volsegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_segmentation: Full path of input segmentation.
+        output_segmentation: Output segmentation file.
+        source_segmentation: Source subcortical volume segmentation file\
+            (instead of using subcortical segs in input segmentation).
+        lh_white_surf: White surface for left hemisphere.
+        lh_pial_surf: Pial surface for left hemisphere.
+        rh_white_surf: White surface for right hemisphere.
+        rh_pial_surf: Pial surface for right hemisphere.
+        lh_cortex_mask: Mask for left hemisphere cortex (usually\
+            lh.cortex.label).
+        rh_cortex_mask: Mask for right hemisphere cortex (usually\
+            rh.cortex.label).
+        fix_presurf_ribbon: Fix the cortical and WM labels in the input\
+            segmentation using ribbon file.
+        label_cortex: Relabel cortex in the input segmentation with surface\
+            annotation.
+        label_wm: Relabel cerebral WM in the input segmentation with surface\
+            annotation.
+        label_wm_unknown: Relabel unknown WM as lhval and rhval (default is\
+            5001 and 5002).
+        lh_annotation: Left hemisphere annotation for --label-cortex and\
+            --label-wm.
+        rh_annotation: Right hemisphere annotation for --label-cortex and\
+            --label-wm.
+        wmparc_dmax: Max distance (mm) from cortex to be labeled as gyral WM.
+        rip_unknown: Do not label WM based on 'unknown' cortical label.
+        hypo_as_wm: Label hypointensities as WM (when fixing with ribbon).
+        hashres: Surface hash table resolution.
+        nhops: Number of surface hops when searching for a nearby annotation.
+        help_flag: Print out information on how to use this program.
+        version_flag: Print out version and exit.
+        crs_test: Test labeling of only the voxel given by column, row, slice\
+            (debugging).
+        ctab_file: Embed color table in the output.
+        threads_number: Run in parallel with the specified number of threads.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_surf2volseg",
+        "label_cortex": label_cortex,
+        "label_wm": label_wm,
+        "rip_unknown": rip_unknown,
+        "hypo_as_wm": hypo_as_wm,
+        "help_flag": help_flag,
+        "version_flag": version_flag,
+    }
+    if input_segmentation is not None:
+        params["input_segmentation"] = input_segmentation
+    if output_segmentation is not None:
+        params["output_segmentation"] = output_segmentation
+    if source_segmentation is not None:
+        params["source_segmentation"] = source_segmentation
+    if lh_white_surf is not None:
+        params["lh_white_surf"] = lh_white_surf
+    if lh_pial_surf is not None:
+        params["lh_pial_surf"] = lh_pial_surf
+    if rh_white_surf is not None:
+        params["rh_white_surf"] = rh_white_surf
+    if rh_pial_surf is not None:
+        params["rh_pial_surf"] = rh_pial_surf
+    if lh_cortex_mask is not None:
+        params["lh_cortex_mask"] = lh_cortex_mask
+    if rh_cortex_mask is not None:
+        params["rh_cortex_mask"] = rh_cortex_mask
+    if fix_presurf_ribbon is not None:
+        params["fix_presurf_ribbon"] = fix_presurf_ribbon
+    if label_wm_unknown is not None:
+        params["label_wm_unknown"] = label_wm_unknown
+    if lh_annotation is not None:
+        params["lh_annotation"] = lh_annotation
+    if rh_annotation is not None:
+        params["rh_annotation"] = rh_annotation
+    if wmparc_dmax is not None:
+        params["wmparc_dmax"] = wmparc_dmax
+    if hashres is not None:
+        params["hashres"] = hashres
+    if nhops is not None:
+        params["nhops"] = nhops
+    if crs_test is not None:
+        params["crs_test"] = crs_test
+    if ctab_file is not None:
+        params["ctab_file"] = ctab_file
+    if threads_number is not None:
+        params["threads_number"] = threads_number
+    return params
+
+
+def mri_surf2volseg_cargs(
+    params: MriSurf2volsegParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_surf2volseg")
+    if params.get("input_segmentation") is not None:
+        cargs.extend([
+            "--i",
+            execution.input_file(params.get("input_segmentation"))
+        ])
+    if params.get("output_segmentation") is not None:
+        cargs.extend([
+            "--o",
+            params.get("output_segmentation")
+        ])
+    if params.get("source_segmentation") is not None:
+        cargs.extend([
+            "--src",
+            execution.input_file(params.get("source_segmentation"))
+        ])
+    if params.get("lh_white_surf") is not None:
+        cargs.extend([
+            "--lh-white",
+            execution.input_file(params.get("lh_white_surf"))
+        ])
+    if params.get("lh_pial_surf") is not None:
+        cargs.extend([
+            "--lh-pial",
+            execution.input_file(params.get("lh_pial_surf"))
+        ])
+    if params.get("rh_white_surf") is not None:
+        cargs.extend([
+            "--rh-white",
+            execution.input_file(params.get("rh_white_surf"))
+        ])
+    if params.get("rh_pial_surf") is not None:
+        cargs.extend([
+            "--rh-pial",
+            execution.input_file(params.get("rh_pial_surf"))
+        ])
+    if params.get("lh_cortex_mask") is not None:
+        cargs.extend([
+            "--lh-cortex-mask",
+            execution.input_file(params.get("lh_cortex_mask"))
+        ])
+    if params.get("rh_cortex_mask") is not None:
+        cargs.extend([
+            "--rh-cortex-mask",
+            execution.input_file(params.get("rh_cortex_mask"))
+        ])
+    if params.get("fix_presurf_ribbon") is not None:
+        cargs.extend([
+            "--fix-presurf-with-ribbon",
+            execution.input_file(params.get("fix_presurf_ribbon"))
+        ])
+    if params.get("label_cortex"):
+        cargs.append("--label-cortex")
+    if params.get("label_wm"):
+        cargs.append("--label-wm")
+    if params.get("label_wm_unknown") is not None:
+        cargs.extend([
+            "--label-wm-unknown",
+            *map(str, params.get("label_wm_unknown"))
+        ])
+    if params.get("lh_annotation") is not None:
+        cargs.extend([
+            "--lh-annot",
+            execution.input_file(params.get("lh_annotation"))
+        ])
+    if params.get("rh_annotation") is not None:
+        cargs.extend([
+            "--rh-annot",
+            execution.input_file(params.get("rh_annotation"))
+        ])
+    if params.get("wmparc_dmax") is not None:
+        cargs.extend([
+            "--wmparc-dmax",
+            str(params.get("wmparc_dmax"))
+        ])
+    if params.get("rip_unknown"):
+        cargs.append("--rip-unknown")
+    if params.get("hypo_as_wm"):
+        cargs.append("--hypo-as-wm")
+    if params.get("hashres") is not None:
+        cargs.extend([
+            "--hashres",
+            str(params.get("hashres"))
+        ])
+    if params.get("nhops") is not None:
+        cargs.extend([
+            "--nhops",
+            str(params.get("nhops"))
+        ])
+    if params.get("help_flag"):
+        cargs.append("--help")
+    if params.get("version_flag"):
+        cargs.append("--version")
+    if params.get("crs_test") is not None:
+        cargs.extend([
+            "--crs-test",
+            *map(str, params.get("crs_test"))
+        ])
+    if params.get("ctab_file") is not None:
+        cargs.extend([
+            "--ctab",
+            execution.input_file(params.get("ctab_file"))
+        ])
+    if params.get("threads_number") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads_number"))
+        ])
+    return cargs
+
+
+def mri_surf2volseg_outputs(
+    params: MriSurf2volsegParameters,
+    execution: Execution,
+) -> MriSurf2volsegOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriSurf2volsegOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_surf2volseg_execute(
+    params: MriSurf2volsegParameters,
+    execution: Execution,
+) -> MriSurf2volsegOutputs:
+    """
+    Tool that cleans up presurf aseg cortex and WM, maps cortical labels from an
+    annotation into a volume, and labels cerebral WM with closest cortical label.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSurf2volsegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_surf2volseg_cargs(params, execution)
+    ret = mri_surf2volseg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_surf2volseg(
+    input_segmentation: InputPathType | None = None,
+    output_segmentation: str | None = None,
+    source_segmentation: InputPathType | None = None,
+    lh_white_surf: InputPathType | None = None,
+    lh_pial_surf: InputPathType | None = None,
+    rh_white_surf: InputPathType | None = None,
+    rh_pial_surf: InputPathType | None = None,
+    lh_cortex_mask: InputPathType | None = None,
+    rh_cortex_mask: InputPathType | None = None,
+    fix_presurf_ribbon: InputPathType | None = None,
+    label_cortex: bool = False,
+    label_wm: bool = False,
+    label_wm_unknown: list[float] | None = None,
+    lh_annotation: InputPathType | None = None,
+    rh_annotation: InputPathType | None = None,
+    wmparc_dmax: float | None = None,
+    rip_unknown: bool = False,
+    hypo_as_wm: bool = False,
+    hashres: float | None = None,
+    nhops: float | None = None,
+    help_flag: bool = False,
+    version_flag: bool = False,
+    crs_test: list[float] | None = None,
+    ctab_file: InputPathType | None = None,
+    threads_number: float | None = None,
+    runner: Runner | None = None,
+) -> MriSurf2volsegOutputs:
+    """
+    Tool that cleans up presurf aseg cortex and WM, maps cortical labels from an
+    annotation into a volume, and labels cerebral WM with closest cortical label.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_segmentation: Full path of input segmentation.
+        output_segmentation: Output segmentation file.
+        source_segmentation: Source subcortical volume segmentation file\
+            (instead of using subcortical segs in input segmentation).
+        lh_white_surf: White surface for left hemisphere.
+        lh_pial_surf: Pial surface for left hemisphere.
+        rh_white_surf: White surface for right hemisphere.
+        rh_pial_surf: Pial surface for right hemisphere.
+        lh_cortex_mask: Mask for left hemisphere cortex (usually\
+            lh.cortex.label).
+        rh_cortex_mask: Mask for right hemisphere cortex (usually\
+            rh.cortex.label).
+        fix_presurf_ribbon: Fix the cortical and WM labels in the input\
+            segmentation using ribbon file.
+        label_cortex: Relabel cortex in the input segmentation with surface\
+            annotation.
+        label_wm: Relabel cerebral WM in the input segmentation with surface\
+            annotation.
+        label_wm_unknown: Relabel unknown WM as lhval and rhval (default is\
+            5001 and 5002).
+        lh_annotation: Left hemisphere annotation for --label-cortex and\
+            --label-wm.
+        rh_annotation: Right hemisphere annotation for --label-cortex and\
+            --label-wm.
+        wmparc_dmax: Max distance (mm) from cortex to be labeled as gyral WM.
+        rip_unknown: Do not label WM based on 'unknown' cortical label.
+        hypo_as_wm: Label hypointensities as WM (when fixing with ribbon).
+        hashres: Surface hash table resolution.
+        nhops: Number of surface hops when searching for a nearby annotation.
+        help_flag: Print out information on how to use this program.
+        version_flag: Print out version and exit.
+        crs_test: Test labeling of only the voxel given by column, row, slice\
+            (debugging).
+        ctab_file: Embed color table in the output.
+        threads_number: Run in parallel with the specified number of threads.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSurf2volsegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SURF2VOLSEG_METADATA)
+    params = mri_surf2volseg_params(
+        input_segmentation=input_segmentation,
+        output_segmentation=output_segmentation,
+        source_segmentation=source_segmentation,
+        lh_white_surf=lh_white_surf,
+        lh_pial_surf=lh_pial_surf,
+        rh_white_surf=rh_white_surf,
+        rh_pial_surf=rh_pial_surf,
+        lh_cortex_mask=lh_cortex_mask,
+        rh_cortex_mask=rh_cortex_mask,
+        fix_presurf_ribbon=fix_presurf_ribbon,
+        label_cortex=label_cortex,
+        label_wm=label_wm,
+        label_wm_unknown=label_wm_unknown,
+        lh_annotation=lh_annotation,
+        rh_annotation=rh_annotation,
+        wmparc_dmax=wmparc_dmax,
+        rip_unknown=rip_unknown,
+        hypo_as_wm=hypo_as_wm,
+        hashres=hashres,
+        nhops=nhops,
+        help_flag=help_flag,
+        version_flag=version_flag,
+        crs_test=crs_test,
+        ctab_file=ctab_file,
+        threads_number=threads_number,
+    )
+    return mri_surf2volseg_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SURF2VOLSEG_METADATA",
+    "MriSurf2volsegOutputs",
+    "MriSurf2volsegParameters",
+    "mri_surf2volseg",
+    "mri_surf2volseg_params",
+]

niwrap_freesurfer/freesurfer/mri_surfacemask.py

@@ -0,0 +1,196 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_SURFACEMASK_METADATA = Metadata(
+    id="b54f5cc796265da710c425a288cee6461dd77a00.boutiques",
+    name="mri_surfacemask",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriSurfacemaskParameters = typing.TypedDict('MriSurfacemaskParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_surfacemask"],
+    "input_volume": InputPathType,
+    "input_surface": InputPathType,
+    "output_volume": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_surfacemask": mri_surfacemask_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "mri_surfacemask": mri_surfacemask_outputs,
+    }.get(t)
+
+
+class MriSurfacemaskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_surfacemask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_volume_file: OutputPathType
+    """The resulting surface-masked volume"""
+
+
+def mri_surfacemask_params(
+    input_volume: InputPathType,
+    input_surface: InputPathType,
+    output_volume: str,
+) -> MriSurfacemaskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_volume: Input volume which will be masked.
+        input_surface: Surface file used for masking the volume.
+        output_volume: Output volume file where pixels outside the surface are\
+            set to zero.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_surfacemask",
+        "input_volume": input_volume,
+        "input_surface": input_surface,
+        "output_volume": output_volume,
+    }
+    return params
+
+
+def mri_surfacemask_cargs(
+    params: MriSurfacemaskParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_surfacemask")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.append(execution.input_file(params.get("input_surface")))
+    cargs.append(params.get("output_volume"))
+    return cargs
+
+
+def mri_surfacemask_outputs(
+    params: MriSurfacemaskParameters,
+    execution: Execution,
+) -> MriSurfacemaskOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriSurfacemaskOutputs(
+        root=execution.output_file("."),
+        output_volume_file=execution.output_file(params.get("output_volume")),
+    )
+    return ret
+
+
+def mri_surfacemask_execute(
+    params: MriSurfacemaskParameters,
+    execution: Execution,
+) -> MriSurfacemaskOutputs:
+    """
+    Tool to produce a new volume where all pixels outside the surface are set to
+    zero.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriSurfacemaskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_surfacemask_cargs(params, execution)
+    ret = mri_surfacemask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_surfacemask(
+    input_volume: InputPathType,
+    input_surface: InputPathType,
+    output_volume: str,
+    runner: Runner | None = None,
+) -> MriSurfacemaskOutputs:
+    """
+    Tool to produce a new volume where all pixels outside the surface are set to
+    zero.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_volume: Input volume which will be masked.
+        input_surface: Surface file used for masking the volume.
+        output_volume: Output volume file where pixels outside the surface are\
+            set to zero.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriSurfacemaskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SURFACEMASK_METADATA)
+    params = mri_surfacemask_params(
+        input_volume=input_volume,
+        input_surface=input_surface,
+        output_volume=output_volume,
+    )
+    return mri_surfacemask_execute(params, execution)
+
+
+__all__ = [
+    "MRI_SURFACEMASK_METADATA",
+    "MriSurfacemaskOutputs",
+    "MriSurfacemaskParameters",
+    "mri_surfacemask",
+    "mri_surfacemask_params",
+]